Utility (utils) module
PyMIALSRTK utils functions.
- pymialsrtk.interfaces.utils.get_emission_car_miles_equivalent(emissions)[source]
Return the equivalent of CO2 emissions [Kg] in terms of kms traveled by an average car.
References
- pymialsrtk.interfaces.utils.get_emission_tv_time_equivalent(emissions)[source]
Return the equivalent of CO2 emissions [Kg] in terms of kms traveled by an average car.
References
- pymialsrtk.interfaces.utils.reorder_by_run_ids(p_files, p_order)[source]
Function used to reorder images by their run-id IDS tag.
The images are sorted according to the input parameters. If more images are available, they remaining are sorted in scending order.
- Parameters
p_files (list of string) – List of image paths - containing a ‘run-’ id tag, to be reordered
p_order (list of int) – List of expecting run id order.
Examples
>>> in_files = ['sub-01_run-2_T2w.nii.gz', 'sub-01_run-5_T2w.nii.gz', 'sub-01_run-3_T2w.nii.gz', 'sub-01_run-1_T2w.nii.gz'] >>> my_order = [1,5,3] >>> reorder_by_run_ids(in_files, my_order)
- pymialsrtk.interfaces.utils.run(command, env=None, cwd=None)[source]
Function calls by each MIALSRTK interface.
It runs the command specified as input via
subprocess.run().- Parameters
command (string) – String containing the command to be executed (required)
env (os.environ) – Specify a custom os.environ
cwd (Directory) – Specify a custom current working directory
Examples
>>> cmd = 'btkNLMDenoising -i "/path/to/in_file" -o "/path/to/out_file" -b 0.1' >>> run(cmd)
- pymialsrtk.interfaces.utils.sort_ascending(p_files)[source]
Function used to sort images at the input of a nipype node.
- Parameters
p_files (list) – List of image paths to be sorted in ascending order
Examples
>>> in_files = ['sub-01_run-2_T2w.nii.gz', 'sub-01_run-5_T2w.nii.gz', 'sub-01_run-3_T2w.nii.gz', 'sub-01_run-1_T2w.nii.gz'] >>> sort_ascending(in_files)